Earlier, at the NATO meeting in Brussels, a clearly irritated Russian Foreign Minister Sergei Lavrov questioned a statement by Western diplomats supporting Ukraine's aspirations for a European future. He said the unrest in Kiev should be dealt with internally.
"I hope Ukranian politicians will be able to bring this situation back on a constitutional track," Lavrov said. "And we encourage everybody not to interfere."
Moldovan officials say Russia's attempts to retain influence in Chisinau have been clear.
Moscow banned Moldovan wine and brandy imports in September in a direct hit to Moldova's economy. Russia said the embargo was the result of the drinks' substandard quality, but it was viewed by many as a warning shot to dissuade Moldova from signing the EU agreement. An estimated $61 million in Moldovan wine was sold in Russia last year.
U.S. officials said Moldova, an agricultural country of about 3 million people, is Europe's poorest nation with an annual gross domestic product of $7.25 billion.
Russia "tried to thwart us signing the association with the EU and influence the results of the elections in our country and will do so when elections take place in a year," Moldovan President Nicolae Timofti told Kerry in an appeal for stronger U.S. assistance in regional security.
He added: "Moldova has committed itself to actively contribute to promoting democracy and security internally, and internationally with our western partners."
Kerry sought to step into the economic breach with plans to increase trade opportunities for Moldovan wine, fashion and other goods. It provided a comfortable cocktail hour travel break for Kerry, who is dealing with a tentative U.S. military future of Afghanistan and foundering peace talks between Israel and Palestinians.
Kerry originally planned to visit Kiev and participate in a meeting of foreign ministers from the Organization of Security and Cooperation in Europe, during this weeklong trip that took him from Brussels to Jerusalem.
However, following Kiev's rejection of the EU agreement and subsequent protests, the State Department said scheduling reasons would prevent Kerry from attending. The department has refused to elaborate on the scheduling problem, and U.S. officials have privately allowed that the cancellation was a sign of displeasure with the Ukrainian government.
Vice President Joe Biden visited Chisinau two years ago, but Kerry's trip marked the first trip to Moldova by a U.S. secretary of state since 1992.
At the wine cellar, which stores an estimated 1.3 million bottles, Moldova Agriculture Minister Vasile Bumacor said the industry has not done a good job of marketing in the West. The Cricova winery, he said, "used to be so famous in the USSR area, they forgot to promote in the West."
"I hope with the assistance of the (U.S.) embassy, we will move toward the West," Bumacor said.
Kerry quipped back: "We like the Russians, but we don't want to leave them all the wine."
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Associated Press writers Matthew Lee in Washington and Alison Mutler in Bucharest, Romania, contributed to this report.